Merge remote-tracking branch 'neurom/master'

package.json

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+{
+  "name": "NeuroM",
+  "description": "NeuroM is a Python toolkit for the analysis and processing of neuron morphologies.",
+  "version": "1.4.2",
+  "scripts": {
+    "build_doc": "echo 'neurom.readthedocs.io/en/latest'"
+  },
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/BlueBrain/NeuroM/releases",
+    "issuesurl": "https://github.com/BlueBrain/NeuroM/issues"
+  },
+  "author": "Michael Gevaert, Lida Kanari, Juan Palacios, Eleftherios Zisis",
+  "contributors": ["Oren Amsalem", "Jean-Denis Courcol", "Michael Gevaert", "Lida Kanari", "Juan Palacios", "Arseny Povolotsky", "Liesbeth Vanherpe", "Eleftherios Zisis"],
+  "license": "BSD 3-Clause"
+}

tutorial/neurom_tutorial.rst

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+===============
+NeuroM Tutorial
+===============
+
+1. Installation instructions
+============================
+
+`NeuroM <http://neurom.readthedocs.io/en/latest/index.html>`__ is a
+Python-based toolkit for the analysis and processing of neuron
+morphologies. It is supported for Linux and OS X. Windows users are
+advised to use `VirtualBox <https://www.virtualbox.org/>`__. More
+detailed installation instructions can be found
+`here <http://neurom.readthedocs.io/en/latest/install.html>`__.
+
+1.1 Requirements
+----------------
+
+It is assumed that the following packages are installed on your system:
+
+- Python >= 2.7
+- pip >= 8.1.0
+- ipython
+- virtualenv
+
+These are available as packages in most Linux distributions. For OS X,
+please refer to `MacPorts <http://www.macports.org/>`__ if you don't
+already use a different package manager.
+
+The following Python packages will be installed automatically with
+NeuroM if not pre-installed in your system:
+
+- numpy >= 1.8.0
+- scipy >= 0.17.0
+- h5py >= 2.2.1 (optional)
+- matplotlib >= 1.3.1
+- pyyaml >= 3.10
+- enum34 >= 1.0.4
+- tqdm >= 4.8.4
+- future >= 0.16.0
+- pylru >= 1.0
+
+1.2 Virtual environment set-up
+------------------------------
+
+It is recommended that you install NeuroM into a virtual environment.
+
+::
+
+    $ virtualenv nrm                           # creates a virtualenv called "nrm" in nrm directory
+    $ source nrm/bin/activate                  # activates virtualenv
+    (nrm)$                                     # now we are in the nrm virtualenv
+
+The prompt indicates that the virtual environment has been activated. To
+de-activate it:
+
+::
+
+    (nrm)$ deactivate
+
+
+1.3 Installation from source
+----------------------------
+
+Clone the NeuroM repository and install it:
+
+::
+
+    (nrm)$ git clone https://github.com/BlueBrain/NeuroM.git
+    (nrm)$ pip install --upgrade pip           # install newest pip inside virtualenv if version too old
+    (nrm)$ pip install -e ./NeuroM             # the -e flag makes source changes immediately effective
+
+2. Applications using NeuroM
+============================
+
+NeuroM ships with configurable command line applications for commonly
+needed functionality.
+
+2.1 morph_check: check the validity of a morphology file
+--------------------------------------------------------
+
+The application
+`morph_check <http://neurom.readthedocs.io/en/latest/morph_check.html>`__
+allows you to apply semantic checks to a morphology file before loading
+it into NeuroM:
+
+::
+
+    (nrm)$ morph_check -h                      # shows help for morphology checking script
+
+Try it yourself! You can go to
+`NeuroMorpho.Org <http://neuromorpho.org>`__ to download a neuronal
+morphology and perform the semantic checks:
+
+::
+
+    (nrm)$ morph_check  path/to/files/filename
+
+2.2 morph_stats: extract basic morphometrics of a sample morphology
+-------------------------------------------------------------------
+
+The application
+`morph_stats <http://neurom.readthedocs.io/en/latest/morph_stats.html>`__
+extracts various morphometrics for one or many morphologies. Its
+contents can be easily configured via a configuration file, as shown in
+the `online
+documentation <http://neurom.readthedocs.io/en/latest/morph_stats.html>`__.
+
+::
+
+    (nrm)$ morph_stats -h                      # shows help for the morphometrics extraction script
+    (nrm)$ morph_stats path/to/files/filename  # analyze single morphology file
+    (nrm)$ morph_stats path/to/files           # analyze many morphology files
+
+3. The NeuroM Tutorial Notebook
+===============================
+
+In the NeuroM repository, you will find a folder ``tutorial``, which
+contains a tutorial notebook on NeuroM. For a detailed explanation on
+installing and running Jupyter/IPython notebooks, we refer to `the
+Jupyter/IPython Notebook Quick Start
+Guide <https://jupyter-notebook-beginner-guide.readthedocs.io/en/latest/>`__.
+
+First, install ``jupyter`` in the virtual environment. Second, launch
+the Jupyter Notebook App. Make sure that you launch the application from
+a folder that contains the NeuroM Tutorial notebook.
+
+::
+
+    (nrm)$ pip install jupyter
+    (nrm)$ cd /path/to/dir/containing/notebook
+    (nrm)$ jupyter notebook                    # launch the Jupyter Notebook App
+
+Next, you can select the notebook that you want to open. Now, you can go
+through the tutorial and learn about loading, viewing, and analyzing
+neuronal morphologies!